[English] 日本語
Yorodumi
- PDB-5v7z: SSNMR Structure of the Human RIP1/RIP3 Necrosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v7z
TitleSSNMR Structure of the Human RIP1/RIP3 Necrosome
Components
  • PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
  • THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
KeywordsSIGNALING PROTEIN / signaling complex / human functional amyloid
Function / homology
Function and homology information


regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / regulation of adaptive immune response / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of type II interferon production / TLR3-mediated TICAM1-dependent programmed cell death / activation of protein kinase activity / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of macrophage differentiation / T cell apoptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / non-canonical NF-kappaB signal transduction / positive regulation of programmed necrotic cell death / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / response to tumor necrosis factor / T cell homeostasis / positive regulation of execution phase of apoptosis / canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / extrinsic apoptotic signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / reactive oxygen species metabolic process / thymus development / Regulation of TNFR1 signaling / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / apoptotic signaling pathway / Regulation of necroptotic cell death / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / protein modification process / SARS-CoV-1 activates/modulates innate immune responses / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / Ovarian tumor domain proteases / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / T cell differentiation in thymus / positive regulation of neuron apoptotic process / protein autophosphorylation / response to oxidative stress / regulation of apoptotic process / defense response to virus / amyloid fibril formation / Potential therapeutics for SARS / transcription coactivator activity / endosome membrane / receptor complex / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity
Similarity search - Function
RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain ...RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 1 / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics / molecular dynamics
AuthorsMompean, M. / Li, W. / Li, J. / Laage, S. / Siemer, A.B. / Wu, H. / McDermott, A.E.
CitationJournal: Cell / Year: 2018
Title: The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex.
Authors: Mompean, M. / Li, W. / Li, J. / Laage, S. / Siemer, A.B. / Bozkurt, G. / Wu, H. / McDermott, A.E.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
B: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
C: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
D: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
E: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
F: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
G: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
H: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE


Theoretical massNumber of molelcules
Total (without water)14,5168
Polymers14,5168
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9690 Å2
ΔGint-48 kcal/mol
Surface area8380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1target function

-
Components

#1: Protein/peptide
PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP


Mass: 1577.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y572*PLUS
#2: Protein/peptide
THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE


Mass: 2051.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13546*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1DARR 250 MS
122isotropic1DARR 250 MS
133isotropic1DARR 250 MS
141isotropic2CHHC 500 US
153isotropic2CHHC 500 US
162isotropic2PAR 15 MS
173isotropic2PAR 15 MS
182isotropic2PAIN 6 MS
193isotropic2PAIN 6 MS
1101isotropic2TEDOR 8 MS
1112isotropic2TEDOR 8 MS
1123isotropic2TEDOR 8 MS
1131isotropic2NCOCX
1141isotropic2NCOCA
1151isotropic2NCACX
1161isotropic2NCA
1171isotropic1DARR 50 MS
1182isotropic1DARR 50 MS
1193isotropic1DARR 50 MS
1201isotropic1DARR 20 MS
1212isotropic1DARR 20 MS
1223isotropic1DARR 20 MS
1231isotropic1DARR 100 MS
1242isotropic1DARR 100 MS
1253isotropic1DARR 100 MS
1261isotropic1DARR 500 MS
1272isotropic1DARR 500 MS
1283isotropic1DARR 500 MS

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
fiber115 mg/mL [U-100% 13C; U-100% 15N] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
fiber215 mg/mL [U-100% 15N; 2-13C-GLYCEROL] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
fiber315 mg/mL [U-100% 15N; 1,3-13C-GLYCEROL] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLRIP1/RIP3[U-100% 13C; U-100% 15N]1
15 mg/mLRIP1/RIP3[U-100% 15N; 2-13C-GLYCEROL]2
15 mg/mLRIP1/RIP3[U-100% 15N; 1,3-13C-GLYCEROL]3
Sample conditionsIonic strength: 0 Not defined / Label: CONDITIONS_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCEBrukerAVANCE7502

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
torsion angle dynamics1
molecular dynamics2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more